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Synthetic Biologists Demonstrate Ability to Rapidly Create Cheap, Accurate In Vitro Diagnostics Tests That Could Eventually Help Pathologists Diagnose Disease | Dark Daily

Synthetic Biologists Demonstrate Ability to Rapidly Create Cheap, Accurate In Vitro Diagnostics Tests That Could Eventually Help Pathologists Diagnose Disease | Dark Daily | SynBioFromLeukipposInstitute | Scoop.it
One goal of many synthetic biology researchers is to create in vitro diagnostic testing systems that produce results that are as accurate as those produced in today’s state-of-the-art clinical pathology laboratories, yet are much cheaper to run because they incorporate low-cost materials, such as paper.
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Engineering Aptazyme Switches for Conditional Gene Expression in Mammalian Cells Utilizing an In Vivo Screening Approach - Springer

Engineering Aptazyme Switches for Conditional Gene Expression in Mammalian Cells Utilizing an In Vivo Screening Approach - Springer | SynBioFromLeukipposInstitute | Scoop.it
Artificial RNA switches are an emerging class of genetic controllers suitable for synthetic biology applications. Aptazymes are fusions composed of an aptamer domain and a self-cleaving ribozyme. The utilization of aptazymes for conditional gene expression displays several advantages over employing conventional transcription factor-based techniques as aptazymes require minimal genomic space, fulfill their function without the need of protein cofactors, and most importantly are reprogrammable with respect to ligand selectivity and the RNA function to be regulated. Technologies that enable the generation of aptazymes to defined input ligands are of interest for the construction of biocomputing devices and biosensing applications. In this chapter we present a method that facilitates the in vivo screening of randomized pools of aptazymes in mammalian cells
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In vivo programmed gene expression based on artificial quorum networks.

Quorum sensing system, as a well-functioned population-dependent gene switch, has been widely applied in many gene circuits in synthetic biology. In our work, an efficient cell density-controlled expression system (QS) was established via engineering Vibrio fischeri luxI-luxR quorum sensing system. In order to achieve in vivo programmed gene expression, a synthetic binary regulation circuit (araQS) was constructed by assembling multiple genetic components including quorum quenching protein AiiA and arabinose promoter ParaBAD into the QS system. In vitro expression assay verified that the araQS system was only initiated in the absence of arabinose in the medium at high cell density. In vivo expression assay confirmed that the araQS system presented an in vivo-triggered and cell density-dependent expression pattern. Furthermore, the araQS system was demonstrated to function well in different bacteria, indicating a wide range of bacterial hosts for use. To explore its potential applications in vivo, the araQS system was used to control the production of a heterologous protective antigen in an attenuated Edwardsiella tarda, which successfully evoked efficient immune protection in fish model. This work suggested that the araQS system could program bacterial expression in vivo and might have potential uses, including, but not limited to, bacterial vector vaccine.
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Jennifer Doudna, a Pioneer Who Helped Simplify Genome Editing

Jennifer Doudna, a Pioneer Who Helped Simplify Genome Editing | SynBioFromLeukipposInstitute | Scoop.it
The biochemist at the University of California, Berkeley, helped make a monumental discovery: a relatively simple way to alter any organism’s DNA. But she is stuck in a patent fight over it.
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A few words about the intersection between art/design and science/synthetic biology

A few words about the intersection between art/design and science/synthetic biology | SynBioFromLeukipposInstitute | Scoop.it
Socrates Logos's insight:
*Art and Synthetic Biology*
 
The question about how art and science interact, and if art is an integrated part of scientific work, or should be banned from science, leads us back to discussions of the ancient Greek philosophers and their precursors. The fundamental question was: What is reality? Can we understand the world around us with the help of our senses, or is the world around us a product of our mental concepts? The answers to these questions never were straightforward, and have been heavily discussed during the last 2000 years. During the different periods of history, sometimes it was en vogue to believe that reality is defined by our senses (materialism) other times people preferred to believe that reality is mental (idealism). 
The concept of idealism was profoundly formulated for the first time by Plato (428/7 - 348/7 BC). Later it was enlivened by different Neo-Platonic movements. E.g. Leonardo Da Vinci (1452 –1519), a follower of Neo-Platonism, did not make a clear distinction between art and science. If the reality of the world basically is a mental product, all mental products including art, play an as equally important role.
Idealistic scientific thinking fell out of favor by the end of the nineteenth century. The main paradigm was now materialism. Idealistic thinking was highly criticized as unscientific. The external world and its observation by experiments became the main subject of science. Reflection about how our brain is structuring the world, and its meaning for scientific discovery were excluded from scientific methodology. Materialistic, scientific approach survived as a leading paradigm until today. Such materialistic orientated science banned art and artistic thinking from science. Art was viewed as a separate area, which could not give valuable contributions to scientific discovery.
However, a number of twentieth century scientists are known to have concerned themselves with Neo-Platonic, artistic thinking, such as earlier described in e.g. Goethes (1749 – 1832) theory of color, a theory focused on the mental reception of color. Among these modern scientists are the logician and mathematician Kurt Goedel (1906 - 1978), the theoretical physicist Werner Heisenberg (1901 - 1976) the mathematical physicist and pioneer of chaos theory Mitchell Feigenbaum (born 1944), to mention a few. Feigenbaum has even said, “Goethe was right about color”! All the above-mentioned use mathematics as their scientific tool. Only mathematics and mathematical logic survived as a respectable science as the paradigm changed to materialism at the turn of the nineteenth century. Mathematics is a product of our brain and thus conceptually idealistic. On first sight a modern eye will often judge idealistic concepts as quite fantastic, naive, strange and far away from all reality. A modern scientist would use exactly these descriptions hearing what Plato claims in his Timaeus; the world is built out of triangles. However, this becomes less suspicious, if one stops to focus on the triangles and starts to reflect over the basic idea behind this concept. In modern theoretical physics we can find such thinking. In quantum theory, as an example, a mathematical model is used to describe the material world of atoms. The Schrödinger equation plays a central role in this theory. The sine function stands central in the solution of this equation. The sine is a function of an angle in the right triangle. So even with his triangles Plato might not have been so wrong and naive as it initially may look. 
Neo-Platonic thinking in science again became acceptable during the last decades. E.g. Norbert Wiener (1894 - 1964, an American mathematician) reintroduced the concept self-organization in 1965 in the second edition of his "Cybernetics: or Control and Communication in the Animal and the Machine" During the years following this publication, the concept of self-organization became popular among scientist working in the field of complex systems. The work of Wiener was influential for the development and understanding of scientific concepts about complex systems. These concepts play an important role in modern scientific movements such as systems biology and synthetic biology. 
Conceptual thinking plays an important role in the contemporary design and art movements. A new intersection between science and art is taking place, since scientific thinking is re-opened for such idealistic concepts. In the following years it will be interesting to see how design and art will influence the development of the field of synthetic biology and vice versa.
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BMC Bioinformatics | Abstract | Pydna: a simulation and documentation tool for DNA assembly strategies using python

Recent advances in synthetic biology have provided tools to efficiently construct complex DNA molecules which are an important part of many molecular biology and biotechnology projects. The planning of such constructs has traditionally been done manually using a DNA sequence editor which becomes error-prone as scale and complexity of the construction increase. A human-readable formal description of cloning and assembly strategies, which also allows for automatic computer simulation and verification, would therefore be a valuable tool.
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Designed Regular Tetragon-Shaped RNA-Protein Complexes with Ribosomal Protein L1 for Bionanotechnology and Synthetic Biology

Designed Regular Tetragon-Shaped RNA-Protein Complexes with Ribosomal Protein L1 for Bionanotechnology and Synthetic Biology | SynBioFromLeukipposInstitute | Scoop.it
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Certificate in Synthetic Biology | Synberc

Certificate in Synthetic Biology | Synberc | SynBioFromLeukipposInstitute | Scoop.it
RT @synberc: Did you know that Synberc offers a Certificate in Synthetic Biology to US undergrads? http://t.co/sR4p4mgVQG #synbio
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SULSA 2015 - Synthetic Biology Meeting | SULSA

SULSA 2015 - Synthetic Biology Meeting | SULSA | SynBioFromLeukipposInstitute | Scoop.it
Great opportunity to give a talk or present a poster @SULSAtweets 2015 Synthetic Biology Meeting http://t.co/kxK5Y1cjk0 Deadline: 15th May
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Exclusive: Apple Pursues DNA Data | MIT Technology Review

Exclusive: Apple Pursues DNA Data | MIT Technology Review | SynBioFromLeukipposInstitute | Scoop.it
The iPhone could become a new tool in genetic studies.
Socrates Logos's insight:

 A very interesting move in respect to personalized medicine. BTW I am working on such an app working in the iPhone, Apple watch environment. I use blockchain technology (Ethereum) to secure DNA data transfer. I will make the App in the first place only available in the US, as there are major legal problems in countries such as Germany. The German government does not trust a citizen to understand his/her medical DNA test results. So, according to the letter of the law: A person who sends his/her DNA to a DNA testing laboratory without the involvement of a Physician will be punished by 1 to 2 year in prison.
http://www.gesetze-im-internet.de/gendg/index.html

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BioBots Is A 3D Printer For Living Cells

BioBots Is A 3D Printer For Living Cells | SynBioFromLeukipposInstitute | Scoop.it
Socrates Logos's insight:

by
Natasha Lomas 

"U.S. biotech startup BioBots sits at the intersection between computer science and chemistry. Its debut product, a desktop 3D printer for biomaterials, which was just demoed on stage at TechCrunch Disrupt NY — printing Van Gogh’s ear in replica, no less — combines hardware, software and wetware. It’s the latter area where the core innovation sits, says co-founder Danny Cabrera.

Biofabrication, the process of artificially building living tissue structures, is not a new field — there is more than a decade of research in this area already. But Cabrera and his co-founders believe they have spotted an opportunity to overhaul expensive (circa $100,000+), large, complex legacy devices — taking inspiration from the small, low-cost desktop 3D printers being used by the maker movement to extrude plastic.
Instead of plastic, BioBots’ 3D printer uses a special ink that can be combined with biomaterials and living cells to build 3D living tissue and miniature human organs. The use-case at this point is for research and pre-clinical screening, such as drug testing (as a replacement for animal testing). It’s not about 3D printing replacement organs from a person’s own cells — albeit developments in this area are heading (incrementally) in that direction. More near term future potential for the tech is to help foster bespoke disease therapies, according to Cabrera...."


 http://tcrn.ch/1INdW7o

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Chinese scientists genetically modify human embryos

Chinese scientists genetically modify human embryos | SynBioFromLeukipposInstitute | Scoop.it
Socrates Logos's insight:
We should not manipulate the germline! 

*Chinese scientists genetically modify human embryos*

by
David Cyranoski& Sara Reardon

"Rumours of germline modification prove true — and look set to reignite an ethical debate.

In a world first, Chinese scientists have reported editing the genomes of human embryos. The results are published1 in the online journal Protein & Cell and confirm widespread rumours that such experiments had been conducted—rumours that  sparked a high-profile debate last month2, 3 about the ethical implications of such work.
In the paper, researchers led by Junjiu Huang, a gene-function researcher at Sun Yat-sen University in Guangzhou, tried to head off such concerns by using 'non-viable' embryos, which cannot result in a live birth, that were obtained from local fertility clinics. The team attempted to modify the gene responsible for β-thalassaemia, a potentially fatal blood disorder, using a gene-editing technique known as CRISPR/Cas9. The researchers say that their results reveal serious obstacles to using the method in medical applications.
"I believe this is the first report of CRISPR/Cas9 applied to human pre-implantation embryos and as such the study is a landmark, as well as a cautionary tale," says George Daley, a stem-cell biologist at Harvard Medical School in Boston. "Their study should be a stern warning to any practitioner who thinks the technology is ready for testing to eradicate disease genes.

Some say that gene editing in embryos could have a bright future because it could eradicate devastating genetic diseases before a baby is born. Others say that such work crosses an ethical line: researchers warned in Nature2 in March that because the genetic changes to embryos, known as germline modification, are heritable, they could have an unpredictable effect on future generations. Researchers have also expressed concerns that any gene-editing research on human embryos could be a slippery slope towards unsafe or unethical uses of the technique.
The paper by Huang's team looks set to reignite the debate on human-embryo editing — and there are reports that other groups in China are also experimenting on human embryos.
Problematic gene
The technique used by Huang’s team involves injecting embryos with the enzyme complex CRISPR/Cas9, which binds and splices DNA at specific locations. The complex can be programmed to target a problematic gene, which is then replaced or repaired by another molecule introduced at the same time. The system is well studied in human adult cell and in animal embryos. But there had been no published reports of its use in human embryos.
Huang and his colleagues set out to see if the procedure could replace a gene in a single-cell fertilized human embryo; in principle, all cells produced as the embryo developed would then have the repaired gene. The embryos they obtained from the fertility clinics had been created for use in in vitro fertilization but had an extra set of chromosomes, following fertilization by two sperm. This prevents the embryos from resulting in a live birth, though they do undergo the first stages of development.
Huang’s group studied the ability of the CRISPR/Cas9 system to edit the gene called HBB, which encodes the human β-globin protein. Mutations in the gene are responsible for β-thalassaemia.
Serious obstacles
The team injected 86 embryos and then waited 48 hours, enough time for the CRISPR/Cas9 system and the molecules that replace the missing DNA to act — and for the embryos to grow to about eight cells each. Of the 71 embryos that survived, 54 were genetically tested. This revealed that just 28 were successfully spliced, and that only a fraction of those contained the replacement genetic material. “If you want to do it in normal embryos, you need to be close to 100%,” Huang says. “That’s why we stopped. We still think it’s too immature.”
His team also found a surprising number of ‘off-target’ mutations assumed to be introduced by the CRISPR/Cas9 complex acting on other parts of the genome. This effect is one of the main safety concerns surrounding germline gene editing because these unintended mutations could be harmful. The rates of such mutations were much higher than those observed in gene-editing studies of mouse embryos or human adult cells. And Huang notes that his team likely only detected a subset of the unintended mutations because their study looked only at a portion of the genome, known as the exome. “If we did the whole genome sequence, we would get many more,” he says.
Ethical questions
Huang says that the paper was rejected by Nature and Science, in part because of ethical objections; both journals declined to comment on the claim (Nature’s news team is editorially independent of its research editorial team.)
He adds that critics of the paper have noted that the low efficiencies and high number of off-target mutations could be specific to the abnormal embryos used in the study. Huang acknowledges the critique, but because there are no examples of gene editing in normal embryos he says that there is no way to know if the technique operates differently in them.
Still, he maintains that the embryos allow for a more meaningful model — and one closer to a normal human embryo — than an animal model or one using adult human cells. “We wanted to show our data to the world so people know what really happened with this model, rather than just talking about what would happen without data,” he says.
But Edward Lanphier, one of the scientists who sounded the warning in Nature last month, says: "It underlines what we said before: we need to pause this research and make sure we have a broad based discussion about which direction we’re going here." Lanphier is president of Sangamo Biosciences in Richmond, California, which applies gene-editing techniques to adult human cells.
......."
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Your Next Prescription Could Be A Genome Sequence

Your Next Prescription Could Be A Genome Sequence | SynBioFromLeukipposInstitute | Scoop.it
Socrates Logos's insight:

by
Meredith Salisbury

"At Advances in Genome Biology and Technology, a conference for genomic scientists held earlier this year, one speaker told attendees that the use of genome sequencing to improve patient care is no longer a far-off goal—it’s happening today. While you won’t encounter genome sequencing on an average visit to the ER, there are certain clinical areas where this technology has indeed become routine: cancer, pediatric care, the diagnosis and treatment of ultra rare diseases, and a few others.

During that same conference, other scientists and doctors recounted impressive cases, from leukemia patients whose cancer was accurately monitored with sequencing to epilepsy patients whose symptoms were successfully treated with a normally unrelated medication chosen because of DNA data. An infant with life-threatening liver failure was restored to health after emergency genome sequencing pinpointed the problem....."


http://onforb.es/1K8aT8T

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RNA Synthetic Biology: From the Test Tube to Cells and Back Again - ACS Synthetic Biology (ACS Publications)

RNA Synthetic Biology: From the Test Tube to Cells and Back Again - ACS Synthetic Biology (ACS Publications) | SynBioFromLeukipposInstitute | Scoop.it
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Stratasys unveils world's first 3D printed wearable, functioning digestive tract

Stratasys unveils world's first 3D printed wearable, functioning digestive tract | SynBioFromLeukipposInstitute | Scoop.it
3D printing vendor Stratsys has unveiled the world's first 3D printed photosynthetic wearable, embedded with living matter.
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THE BIOLOGICAL MICROPROCESSOR on Flipboard

THE BIOLOGICAL MICROPROCESSOR on Flipboard | SynBioFromLeukipposInstitute | Scoop.it
By Gerd Moe-Behrens | Systemics, a revolutionary paradigm shift in scientific thinking, with applications in systems biology, and synthetic biology, have led to the idea of using silicon computers and their engineering principles as a blueprint for the engineering of a similar machine made from biological parts....
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Structures of the CRISPR-Cmr complex reveal mode of RNA target positioning

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 http://bit.ly/1bybhRI

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Biocomputer Meaning

Video shows what biocomputer means. Any of several proposed systems using DNA or proteins to perform data processing (in synthetic biology). Biocomputer ...
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Mitchell Joachim // Synthetic Biology in Design

Mitchell Joachim // Synthetic Biology in Design | SynBioFromLeukipposInstitute | Scoop.it
RT @IAAC: Check out @MitchellJoachim @Terreform_ONE #IAAC #Lecture http://t.co/wvuF5y8iDw #Barcelona #biology #advancedarchitecture #master…
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Biotechnology Will Provide Excellent Investment Opportunities well into the 21st Century

Science Driving Value Creation Much of the science driving biotechnology is still in its earliest stages. We are only at the beginning of finding ways of apply it to medical advances leading to curing disease. Scientists are just scratching the surface in many areas of Hi-Tech medical science, for example researchers [...]
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Sequential growth of long DNA strands with user-defined patterns for nanostructures and scaffolds

Sequential growth of long DNA strands with user-defined patterns for nanostructures and scaffolds | SynBioFromLeukipposInstitute | Scoop.it
Socrates Logos's insight:

by
Graham D. Hamblin, Janane F. Rahbani & Hanadi F. Sleiman

DNA strands of well-defined sequence are valuable in synthetic biology and nanostructure assembly. Drawing inspiration from solid-phase synthesis, here we describe a DNA assembly method that uses time, or order of addition, as a parameter to define structural complexity. DNA building blocks are sequentially added with in-situ ligation, then enzymatic enrichment and isolation. This yields a monodisperse, single-stranded long product (for example, 1,000 bases) with user-defined length and sequence pattern. The building blocks can be repeated with different order of addition, giving different DNA patterns. We organize DNA nanostructures and quantum dots using these backbones. Generally, only a small portion of a DNA structure needs to be addressable, while the rest is purely structural. Scaffolds with specifically placed unique sites in a repeating motif greatly minimize the number of components used, while maintaining addressability. This combination of symmetry and site-specific asymmetry within a DNA strand is easily accomplished with our method."


 http://bit.ly/1FPkfXt

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CRISPR adaptation biases explain preference for acquisition of foreign DNA

CRISPR adaptation biases explain preference for acquisition of foreign DNA | SynBioFromLeukipposInstitute | Scoop.it
Socrates Logos's insight:

by
Asaf Levy, Moran G. Goren, Ido Yosef, Oren Auster, Miriam Manor, Gil Amitai, Rotem Edgar, Udi Qimron & Rotem Sorek

"CRISPR–Cas (clustered, regularly interspaced short palindromic repeats coupled with CRISPR-associated proteins) is a bacterial immunity system that protects against invading phages or plasmids. In the process of CRISPR adaptation, short pieces of DNA (‘spacers’) are acquired from foreign elements and integrated into the CRISPR array. So far, it has remained a mystery how spacers are preferentially acquired from the foreign DNA while the self chromosome is avoided. Here we show that spacer acquisition is replication-dependent, and that DNA breaks formed at stalled replication forks promote spacer acquisition. Chromosomal hotspots of spacer acquisition were confined by Chi sites, which are sequence octamers highly enriched on the bacterial chromosome, suggesting that these sites limit spacer acquisition from self DNA. We further show that the avoidance of self is mediated by the RecBCD double-stranded DNA break repair complex. Our results suggest that, in Escherichia coli, acquisition of new spacers largely depends on RecBCD-mediated processing of double-stranded DNA breaks occurring primarily at replication forks, and that the preference for foreign DNA is achieved through the higher density of Chi sites on the self chromosome, in combination with the higher number of forks on the foreign DNA. This model explains the strong preference to acquire spacers both from high copy plasmids and from phages."

 http://bit.ly/1PnRGTt

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